A Common Type 2 Diabetes Risk Variant Potentiates Activity of an Evolutionarily Conserved Islet Stretch Enhancer and Increases C2CD4A and C2CD4B Expression

Am J Hum Genet. 2018 Apr 5;102(4):620-635. doi: 10.1016/j.ajhg.2018.02.020.


Genome-wide association studies (GWASs) and functional genomics approaches implicate enhancer disruption in islet dysfunction and type 2 diabetes (T2D) risk. We applied genetic fine-mapping and functional (epi)genomic approaches to a T2D- and proinsulin-associated 15q22.2 locus to identify a most likely causal variant, determine its direction of effect, and elucidate plausible target genes. Fine-mapping and conditional analyses of proinsulin levels of 8,635 non-diabetic individuals from the METSIM study support a single association signal represented by a cluster of 16 strongly associated (p < 10-17) variants in high linkage disequilibrium (r2 > 0.8) with the GWAS index SNP rs7172432. These variants reside in an evolutionarily and functionally conserved islet and β cell stretch or super enhancer; the most strongly associated variant (rs7163757, p = 3 × 10-19) overlaps a conserved islet open chromatin site. DNA sequence containing the rs7163757 risk allele displayed 2-fold higher enhancer activity than the non-risk allele in reporter assays (p < 0.01) and was differentially bound by β cell nuclear extract proteins. Transcription factor NFAT specifically potentiated risk-allele enhancer activity and altered patterns of nuclear protein binding to the risk allele in vitro, suggesting that it could be a factor mediating risk-allele effects. Finally, the rs7163757 proinsulin-raising and T2D risk allele (C) was associated with increased expression of C2CD4B, and possibly C2CD4A, both of which were induced by inflammatory cytokines, in human islets. Together, these data suggest that rs7163757 contributes to genetic risk of islet dysfunction and T2D by increasing NFAT-mediated islet enhancer activity and modulating C2CD4B, and possibly C2CD4A, expression in (patho)physiologic states.

Keywords: C2CD4A; C2CD4B; GWAS; NFAT; comparative genomics; inflammation; islet; proinsulin; rs7163757; stretch or super enhancer.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • Alleles
  • Animals
  • Base Sequence
  • Calcium-Binding Proteins / genetics*
  • Calcium-Binding Proteins / metabolism
  • Cell Line
  • Chromatin / metabolism
  • Chromosomes, Human, Pair 15 / genetics
  • Conserved Sequence*
  • Cytokines / metabolism
  • DNA, Intergenic / genetics
  • Enhancer Elements, Genetic / genetics*
  • Evolution, Molecular*
  • Humans
  • Inflammation Mediators / metabolism
  • Islets of Langerhans / pathology*
  • Mice
  • Middle Aged
  • Mutation / genetics*
  • NFATC Transcription Factors / metabolism
  • Nuclear Proteins / genetics*
  • Physical Chromosome Mapping
  • Polymorphism, Single Nucleotide / genetics
  • Proinsulin / metabolism
  • Rats
  • Risk Factors
  • Transcription Factors / genetics*


  • C2CD4A protein, human
  • C2CD4B protein, human
  • Calcium-Binding Proteins
  • Chromatin
  • Cytokines
  • DNA, Intergenic
  • Inflammation Mediators
  • NFATC Transcription Factors
  • Nuclear Proteins
  • Transcription Factors
  • Proinsulin